Elon Musk, the world's richest person and US President Donald Trump's controversial close advisor, said on Monday the giant USAID humanitarian agency will be "shutting down" as part of his drive to shrink the US government.

Hours later, US Secretary of State Marco Rubio indicated it was not disappearing but would come under his control.

"I'm the acting director of USAID," Rubio told reporters on a visit to El Salvador, accusing the agency of "insubordination."

Amid confusion over the future of the US Agency for International Development, employees were instructed by email not to go to their offices Monday. Some 600 staffers found themselves locked out of their computer systems, ABC News reported.

USAID is the aid arm of US foreign policy, funding health and emergency programs in around 120 countries, including the world's poorest regions.

It is also seen as a source of soft power for US foreign policy, which Musk accused of being "corrupt" and involved in an array of political activities.

The SpaceX and Tesla CEO, who has massive contracts with the US government and was the biggest financial backer of Trump's campaign, said he had personally cleared the unprecedented move with the president.

"I went over with him in detail, and he agreed that we should shut it down," Musk said in a discussion on his X online platform.

Meanwhile, Musk's aides have taken control of the US Treasury Department's payments system - which manages trillions of dollars of transactions each year -- sparking alarm among critics. (AFP)